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- PDB-5szu: Novel Structural Insights into GDP-Mediated Regulation of Acyl-Co... -

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Basic information

Entry
Database: PDB / ID: 5szu
TitleNovel Structural Insights into GDP-Mediated Regulation of Acyl-CoA Thioesterases
ComponentsAcyl-CoA hydrolase
KeywordsHYDROLASE / Thioesterase / Nisseria meningitidis / 4HBT / Acyl-CoA thioesterase / Coenzyme A / GDP
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / acyl-CoA metabolic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / cytosol
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Cytosolic acyl coenzyme A thioester hydrolase / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Acyl-CoA hydrolase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKhandokar, Y.B. / Srivastava, P. / Forwood, J.K.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase.
Authors: Khandokar, Y.B. / Srivastava, P. / Cowieson, N. / Sarker, S. / Aragao, D. / Das, S. / Smith, K.M. / Raidal, S.R. / Forwood, J.K.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
C: Acyl-CoA hydrolase
D: Acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0088
Polymers71,9384
Non-polymers3,0704
Water00
1
A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
hetero molecules

A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
hetero molecules

A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,51212
Polymers107,9076
Non-polymers4,6056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area23630 Å2
ΔGint-108 kcal/mol
Surface area36180 Å2
MethodPISA
2
C: Acyl-CoA hydrolase
D: Acyl-CoA hydrolase
hetero molecules

C: Acyl-CoA hydrolase
D: Acyl-CoA hydrolase
hetero molecules

C: Acyl-CoA hydrolase
D: Acyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,51212
Polymers107,9076
Non-polymers4,6056
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area23580 Å2
ΔGint-119 kcal/mol
Surface area35900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.198, 153.198, 153.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein
Acyl-CoA hydrolase


Mass: 17984.541 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria)
Gene: ERS514298_01532, ERS514410_00397, ERS514534_01643, ERS514708_01580, ERS514851_00814
Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: A0A0Y5D4F5, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.17 Å3/Da / Density % sol: 70.49 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris pH 8.5 and 2 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.8→48.45 Å / Num. obs: 28972 / % possible obs: 97.36 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 6.45
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 1.96 / % possible all: 99.66

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IEN

4ien


Resolution: 2.8→48.445 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.22
RfactorNum. reflection% reflection
Rfree0.2138 1444 4.99 %
Rwork0.1701 --
obs0.1723 28955 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 192 0 4808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174900
X-RAY DIFFRACTIONf_angle_d1.5676660
X-RAY DIFFRACTIONf_dihedral_angle_d19.8241880
X-RAY DIFFRACTIONf_chiral_restr0.063748
X-RAY DIFFRACTIONf_plane_restr0.007832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-2.90030.32491420.25172762X-RAY DIFFRACTION100
2.9003-3.01640.28221470.22472799X-RAY DIFFRACTION99
3.0164-3.15370.28391460.20812778X-RAY DIFFRACTION99
3.1537-3.31990.2411240.19292794X-RAY DIFFRACTION99
3.3199-3.52790.23961310.18192793X-RAY DIFFRACTION99
3.5279-3.80020.19921640.15052724X-RAY DIFFRACTION98
3.8002-4.18240.16531440.14442755X-RAY DIFFRACTION98
4.1824-4.78720.17961770.12562715X-RAY DIFFRACTION97
4.7872-6.02950.16221460.14812702X-RAY DIFFRACTION95
6.0295-48.45270.21971230.17122689X-RAY DIFFRACTION90

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